| 1. |
- Andersson, Claes R., et al.
(författare)
-
Revealing cell cycle control by combining model-based detection of periodic expression with novel cis-regulatory descriptors
- 2007
-
Ingår i: BMC Systems Biology. - : Springer Science and Business Media LLC. - 1752-0509. ; 1, s. 45-
-
Tidskriftsartikel (refereegranskat)abstract
- Background: We address the issue of explaining the presence or absence of phase-specific transcription in budding yeast cultures under different conditions. To this end we use a model-based detector of gene expression periodicity to divide genes into classes depending on their behavior in experiments using different synchronization methods. While computational inference of gene regulatory circuits typically relies on expression similarity (clustering) in order to find classes of potentially co-regulated genes, this method instead takes advantage of known time profile signatures related to the studied process. Results: We explain the regulatory mechanisms of the inferred periodic classes with cis-regulatory descriptors that combine upstream sequence motifs with experimentally determined binding of transcription factors. By systematic statistical analysis we show that periodic classes are best explained by combinations of descriptors rather than single descriptors, and that different combinations correspond to periodic expression in different classes. We also find evidence for additive regulation in that the combinations of cis-regulatory descriptors associated with genes periodically expressed in fewer conditions are frequently subsets of combinations associated with genes periodically expression in more conditions. Finally, we demonstrate that our approach retrieves combinations that are more specific towards known cell-cycle related regulators than the frequently used clustering approach. Conclusion: The results illustrate how a model-based approach to expression analysis may be particularly well suited to detect biologically relevant mechanisms. Our new approach makes it possible to provide more refined hypotheses about regulatory mechanisms of the cell cycle and it can easily be adjusted to reveal regulation of other, non-periodic, cellular processes.
|
|
| 2. |
- Gadisa, Abay, et al.
(författare)
-
Transparent polymer cathode for organic photovoltaic devices
- 2006
-
Ingår i: Synthetic metals. - : Elsevier BV. - 0379-6779 .- 1879-3290. ; 156:16-17, s. 1102-1107
-
Tidskriftsartikel (refereegranskat)abstract
- We demonstrate a prototype solar cell with a transparent polymer cathode, and indium-tin-oxide (ITO)/poly (3, 4-ethylene dioxythiophene)-poly (styrene sulphonate) (PEDOT:PSS) anode. As an active layer, thin film of a bulk heterojunction of polyfluorene copolymer poly[2,7-(9,9-dioctyl-fluorene)-alt-5,5-(4′,7′-di-2thienyl-2′,1′3′-benzothiadiazole)] (APFO-3) and an electron acceptor molecule [6] and [6]-phenyl-C61-butyric acid methyl ester (PCBM) (1:4 wt.) was sandwiched between the two transparent polymer electrodes. The cathode is another form of PEDOT formed by vapor phase polymerised PEDOT (VPP PEDOT) of conductivity 102–103 S/cm. The cathode is supported on an elastomeric substrate, and forms a conformal contact to the APFO-3/PCBM blend. Transparent solar cells are useful for building multilayer and tandem solar cells.
|
|
| 3. |
|
|
| 4. |
- Aarnio, H., et al.
(författare)
-
Photoinduced absorption in an alternating polyfluorene copolymer for photovoltaic applications
- 2006
-
Ingår i: Chemical Physics. ; 321:1-2, s. 127-132
-
Tidskriftsartikel (refereegranskat)abstract
- The authors present a detailed study of a novel alternating polyfluorene copolymer, poly[2,7-(9,9-dioctyl-fluorene)-alt-5,5-(4',7'-di-2-thienyl-2',1',3-benzo-thiadiazole)], and its blends with the fullerene deriv. [6,6]-phenyl-C61-butyric acid Me ester, using continuous wave photoinduced absorption (PA) techniques. The authors also present the use of phase information from the PA measurements for estg. the no. of different photoexcitation types present in the PA spectra as well as their lifetimes. In all blends the PA spectra show a broad high-energy PA band ranging from .apprx.1 to 2 eV as well as a low-energy band at .apprx.0.35 eV. The authors find two kinds of excitations present at 80 DegK, polarons showing dispersive recombination with lifetimes of roughly a millisecond, and a 2nd kind of photoexcitation tentatively assigned to coulombically bound intrachain polaron pairs showing practically nondispersive recombination with a lifetime of .apprx.20 ms. [on SciFinder (R)]
|
|
| 5. |
|
|
| 6. |
- Admassie, Shimelis, et al.
(författare)
-
Electrochemical and optical studies of the band gaps of alternating polyfluorene copolymers
- 2006
-
Ingår i: Synthetic metals. - : Elsevier BV. - 0379-6779 .- 1879-3290. ; 156:7-8, s. 614-623
-
Tidskriftsartikel (refereegranskat)abstract
- The electrochemical and optical properties of a series of alternating polyfluorene copolymers with low band gaps were determined. These polymers incorporated fluorene units alternating with groups including electron-withdrawing (A) and electron-donating (D) groups in donor-acceptor-donor (DAD) sequence to achieve the lowering of band gaps. The polymers were solvent-casted on platinum disk electrode and the band gaps were estimated from cyclic voltammetry (CV). These values were compared with values obtained from optical absorption measurements. Although the electrochemically determined band gaps were found to be slightly higher than the optical band gap in most cases, values are well correlated. The values of the band gaps determined range from 2.1 to 1.3 eV. © 2006 Elsevier B.V. All rights reserved.
|
|
| 7. |
- Andersson, Claes R., et al.
(författare)
-
Bayesian detection of periodic mRNA time profiles withouth use of training examples
- 2006
-
Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 7, s. 63-
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Detection of periodically expressed genes from microarray data without use of known periodic and non-periodic training examples is an important problem, e.g. for identifying genes regulated by the cell-cycle in poorly characterised organisms. Commonly the investigator is only interested in genes expressed at a particular frequency that characterizes the process under study but this frequency is seldom exactly known. Previously proposed detector designs require access to labelled training examples and do not allow systematic incorporation of diffuse prior knowledge available about the period time. RESULTS: A learning-free Bayesian detector that does not rely on labelled training examples and allows incorporation of prior knowledge about the period time is introduced. It is shown to outperform two recently proposed alternative learning-free detectors on simulated data generated with models that are different from the one used for detector design. Results from applying the detector to mRNA expression time profiles from S. cerevisiae showsthat the genes detected as periodically expressed only contain a small fraction of the cell-cycle genes inferred from mutant phenotype. For example, when the probability of false alarm was equal to 7%, only 12% of the cell-cycle genes were detected. The genes detected as periodically expressed were found to have a statistically significant overrepresentation of known cell-cycle regulated sequence motifs. One known sequence motif and 18 putative motifs, previously not associated with periodic expression, were also over represented. CONCLUSION: In comparison with recently proposed alternative learning-free detectors for periodic gene expression, Bayesian inference allows systematic incorporation of diffuse a priori knowledge about, e.g. the period time. This results in relative performance improvements due to increased robustness against errors in the underlying assumptions. Results from applying the detector to mRNA expression time profiles from S. cerevisiae include several new findings that deserve further experimental studies.
|
|
| 8. |
- Andersson, Claes R., et al.
(författare)
-
In vitro drug sensitivity-gene expression correlations involve a tissue of origin dependency
- 2007
-
Ingår i: Journal of chemical information and modeling. - : American Chemical Society (ACS). - 1549-9596 .- 1549-960X. ; 47:1, s. 239-248
-
Tidskriftsartikel (refereegranskat)abstract
- A major concern of chemogenomics is to associate drug activity with biological variables. Several reports have clustered cell line drug activity profiles as well as drug activity-gene expression correlation profiles and noted that the resulting groupings differ but still reflect mechanism of action. The present paper shows that these discrepancies can be viewed as a weighting of drug-drug distances, the weights depending on which cell lines the two drugs differ in.
|
|
| 9. |
|
|
| 10. |
- Andersson, R., et al.
(författare)
-
How can regional differences in the risk-of-foreclosure be explained? : Evidence from Swedish single family housing markets
- 2008
-
Ingår i: Journal of Property Research. - : Informa UK Limited. - 0959-9916 .- 1466-4453. ; 25:3, s. 179-202
-
Tidskriftsartikel (refereegranskat)abstract
- In Sweden, quite large differences in the risk-of-foreclosure for single-family housing exist between regions. The aim of this paper is to explain such differences, using data on foreclosures for all Swedish regions. In an option-based model, the risk-of-foreclosure is a function of such things as housing prices and incomes, as well as interest rate and housing price volatility. Instead of using housing prices and incomes to explain the risk of foreclosure, we use explaining variables in the labor market model. The main results indicate that the option-based model explains the variation in foreclosure rates. Specifically, interest rate - together with price volatility, price changes, price and rent level, income, and employment - explains around one-third of the total regional variation. Our extended option-based model explains slightly more. Specialization within the industrial sector seems to have a positive effect on foreclosure risk in that it, together with the educational level of the workforce, reduces the risk. Specifically, mortgage lenders and banks can reduce their risk by concentrating their business on dense regions with a high degree of employment within the manufacturing industry and with a higher educational level of the workforce.
|
|
